COVID-19 OVERVIEW

Genomic surveillance was a significant component of Australia’s response to COVID-19, established in the national approach to surveillance through genomic indicators listed in the ‘Australian National Disease Surveillance Plan for COVID-19’. The CDGN supported the national COVID-19 response through a dedicated working group to monitor SARS-CoV-2 variants to inform Australia’s national approach in detecting and reporting of Variants of Concern (VOC), Variants of Interest (VOI), and Variants Under Monitoring (VUM).

CDGN VOC WORKING GROUP

The CDGN VOC Working Group is responsible for ongoing monitoring and surveillance of SARS-CoV-2 variants literature and global events to inform Australia’s national approach in detecting and reporting of Variants of Concern (VOC), Variants of Interest (VOI) and Variants Under Monitoring (VUM), and mutations of interest reported in the literature. The working group comprised of laboratory and government representatives with expertise in bioinformatics, genomic epidemiology, viral evolution, phylodynamics and medical microbiology.

The CDGN VOC Working Group regularly reviewed and updated the national VOC Laboratory Case Definition and the VOC Literature Summary to ensure the most up to date information is reflected and communicated to the public health laboratories and units. This literature summary was distributed to all jurisdictions across Australia and New Zealand through national committees, the Public Health Laboratory Network (PHLN) and the Communicable Diseases Network of Australia (CDNA). The CDGN VOC Working Group also works closely with the AusTrakka National Analysis Team to ensure timely integration of new VOCs or VOIs that are being monitored and reported in the AusTrakka National VOC reports submitted to the national, state and territory governments on a twice-weekly basis via the Australian Health Protection Principal Committee (AHPPC), PHLN and CDNA.

The CDGN VOC Working Group is still available to support ongoing SARS-CoV-2 surveillance, now shifting to convening on an as-needs basis.

Nationally aggregated sample data

The table below shows the total number of Omicron sequences in Australia categorised as variants of concern, variants of interest and variants under monitoring, as well as the number and proportion of sequences identified for each sub-lineage in the past 28 days.

Data is not equivalent to case numbers, as there may be duplicate sequences for a single case, and not all cases have samples which are able to be sequenced. Sequence numbers may vary from week to week as new sub-lineages are characterised and sequences are re-classified into these new sub-lineages.

^ the number (and percentage) of sequences within the preceding 4 week (28 day) period
~ Inclusive of all XBB* sublineages

Green boxes indicate decreases in proportion compared to previous 28-day period, whereas yellow boxes indicate increases in sequence proportion. VOI and VUMs which have not been observed in the past 8 weeks (including XBF, BR.2, BN.1, BF.7, BA.4.6, BQ.1 and BQ.1.1) have been removed from this table.

Global Overview

SARS-CoV-2 PCR percent positivity, as detected in integrated sentinel surveillance as part of the Global Influenza Surveillance and Response System (GISRS) and reported to FluNet was around 11% as of 3 March 2024.

Globally, JN.1 is the most reported VOI (now reported by 115 countries), accounting for 90.3% of sequences in week 9 compared to 89.4% in week six. Its parent lineage, BA.2.86, is declining and accounted for 2.2% of sequences in week 9 compared to 3.0% in week six.

Globally, the number of new cases decreased by 44% during the past 28-day period of 5 February to 3 March 2024 compared to the previous 28-day period (8 January to 4 February 2024), with over two hundred and ninety-two thousand new cases reported. The number of new deaths decreased by 51% as compared to the previous 28-day period, with 6200 new fatalities reported. As of 3 March 2024, over 774 million confirmed cases and more than seven million deaths have been reported globally.

During the period from 5 February to 3 March 2024, COVID-19 new hospitalizations and admissions to an intensive care unit (ICU) both recorded an overall decrease of 35% and 64% with over 78 000 and 500 admissions, respectively.

This global overview is taken from the latest WHO Coronavirus disease (COVID-19) Epidemiological Update.